GLFNET: Global-Local (frequency) Filter Networks for efficient medical image segmentation

We propose a novel transformer-style architecture called Global-Local Filter Network (GLFNet) for medical image segmentation and demonstrate its state-of-the-art performance. We replace the self-attention mechanism with a combination of global-local filter blocks to optimize model efficiency. The global filters extract features from the whole feature map whereas the local filters are being adaptively created as 4x4 patches of the same feature map and add restricted scale information. In particular, the feature extraction takes place in the frequency domain rather than the commonly used spatial (image) domain to facilitate faster computations. The fusion of information from both spatial and frequency spaces creates an efficient model with regards to complexity, required data and performance. We test GLFNet on three benchmark datasets achieving state-of-the-art performance on all of them while being almost twice as efficient in terms of GFLOP operations.

The legibility of the imaged human brain

Our knowledge of the organisation of the human brain at the population-level is yet to translate into power to predict functional differences at the individual-level, limiting clinical applications, and casting doubt on the generalisability of inferred mechanisms. It remains unknown whether the difficulty arises from the absence of individuating biological patterns within the brain, or from limited power to access them with the models and compute at our disposal. Here we comprehensively investigate the resolvability of such patterns with data and compute at unprecedented scale. Across 23810 unique participants from UK Biobank, we systematically evaluate the predictability of 25 individual biological characteristics, from all available combinations of structural and functional neuroimaging data. Over 4526 GPU*hours of computation, we train, optimize, and evaluate out-of-sample 700 individual predictive models, including multilayer perceptrons of demographic, psychological, serological, chronic morbidity, and functional connectivity characteristics, and both uni- and multi-modal 3D convolutional neural network models of macro- and micro-structural brain imaging. We find a marked discrepancy between the high predictability of sex (balanced accuracy 99.7%), age (mean absolute error 2.048 years, R2 0.859), and weight (mean absolute error 2.609Kg, R2 0.625), for which we set new state-of-the-art performance, and the surprisingly low predictability of other characteristics. Neither structural nor functional imaging predicted individual psychology better than the coincidence of common chronic morbidity (p<0.05). Serology predicted common morbidity (p<0.05) and was best predicted by it (p<0.001), followed by structural neuroimaging (p<0.05). Our findings suggest either more informative imaging or more powerful models will be needed to decipher individual level characteristics from the brain.

mmSense: Detecting Concealed Weapons with a Miniature Radar Sensor

For widespread adoption, public security and surveillance systems must be accurate, portable, compact, and real-time, without impeding the privacy of the individuals being observed. Current systems broadly fall into two categories -- image-based which are accurate, but lack privacy, and RF signal-based, which preserve privacy but lack portability, compactness and accuracy. Our paper proposes mmSense, an end-to-end portable miniaturised real-time system that can accurately detect the presence of concealed metallic objects on persons in a discrete, privacy-preserving modality. mmSense features millimeter wave radar technology, provided by Google's Soli sensor for its data acquisition, and TransDope, our real-time neural network, capable of processing a single radar data frame in 19 ms. mmSense achieves high recognition rates on a diverse set of challenging scenes while running on standard laptop hardware, demonstrating a significant advancement towards creating portable, cost-effective real-time radar based surveillance systems.

Optimizing Vision Transformers for Medical Image Segmentation and Few-Shot Domain Adaptation

The adaptation of transformers to computer vision is not straightforward because the modelling of image contextual information results in quadratic computational complexity with relation to the input features. Most of existing methods require extensive pre-training on massive datasets such as ImageNet and therefore their application to fields such as healthcare is less effective. CNNs are the dominant architecture in computer vision tasks because convolutional filters can effectively model local dependencies and reduce drastically the parameters required. However, convolutional filters cannot handle more complex interactions, which are beyond a small neighbour of pixels. Furthermore, their weights are fixed after training and thus they do not take into consideration changes in the visual input. Inspired by recent work on hybrid visual transformers with convolutions and hierarchical transformers, we propose Convolutional Swin-Unet (CS-Unet) transformer blocks and optimise their settings with relation to patch embedding, projection, the feed-forward network, up sampling and skip connections. CS-Unet can be trained from scratch and inherits the superiority of convolutions in each feature process phase. It helps to encode precise spatial information and produce hierarchical representations that contribute to object concepts at various scales. Experiments show that CS-Unet without pre-training surpasses other state-of-the-art counterparts by large margins on two medical CT and MRI datasets with fewer parameters. In addition, two domain-adaptation experiments on optic disc and polyp image segmentation further prove that our method is highly generalizable and effectively bridges the domain gap between images from different sources.

The Fully Convolutional Transformer for Medical Image Segmentation

We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Networks to learn effective image representations, and combines them with the ability of Transformers to effectively capture long-term dependencies in its inputs. The FCT is the first fully convolutional Transformer model in medical imaging literature. It processes its input in two stages, where first, it learns to extract long range semantic dependencies from the input image, and then learns to capture hierarchical global attributes from the features. FCT is compact, accurate and robust. Our results show that it outperforms all existing transformer architectures by large margins across multiple medical image segmentation datasets of varying data modalities without the need for any pre-training. FCT outperforms its immediate competitor on the ACDC dataset by 1.3%, on the Synapse dataset by 4.4%, on the Spleen dataset by 1.2% and on ISIC 2017 dataset by 1.1% on the dice metric, with up to five times fewer parameters. Our code, environments and models will be available via GitHub.

Rotation Equivariant 3D Hand Mesh Generation from a Single RGB Image

We develop a rotation equivariant model for generating 3D hand meshes from 2D RGB images. This guarantees that as the input image of a hand is rotated the generated mesh undergoes a corresponding rotation. Furthermore, this removes undesirable deformations in the meshes often generated by methods without rotation equivariance. By building a rotation equivariant model, through considering symmetries in the problem, we reduce the need for training on very large datasets to achieve good mesh reconstruction. The encoder takes images defined on $\mathbb{Z}^{2}$ and maps these to latent functions defined on the group $C_{8}$. We introduce a novel vector mapping function to map the function defined on $C_{8}$ to a latent point cloud space defined on the group $\mathrm{SO}(2)$. Further, we introduce a 3D projection function that learns a 3D function from the $\mathrm{SO}(2)$ latent space. Finally, we use an $\mathrm{SO}(3)$ equivariant decoder to ensure rotation equivariance. Our rotation equivariant model outperforms state-of-the-art methods on a real-world dataset and we demonstrate that it accurately captures the shape and pose in the generated meshes under rotation of the input hand.

CpT: Convolutional Point Transformer for 3D Point Cloud Processing

We present CpT: Convolutional point Transformer - a novel deep learning architecture for dealing with the unstructured nature of 3D point cloud data. CpT is an improvement over existing attention-based Convolutions Neural Networks as well as previous 3D point cloud processing transformers. It achieves this feat due to its effectiveness in creating a novel and robust attention-based point set embedding through a convolutional projection layer crafted for processing dynamically local point set neighbourhoods. The resultant point set embedding is robust to the permutations of the input points. Our novel CpT block builds over local neighbourhoods of points obtained via a dynamic graph computation at each layer of the networks' structure. It is fully differentiable and can be stacked just like convolutional layers to learn global properties of the points. We evaluate our model on standard benchmark datasets such as ModelNet40, ShapeNet Part Segmentation, and the S3DIS 3D indoor scene semantic segmentation dataset to show that our model can serve as an effective backbone for various point cloud processing tasks when compared to the existing state-of-the-art approaches.

Survey: Leakage and Privacy at Inference Time

Leakage of data from publicly available Machine Learning (ML) models is an area of growing significance as commercial and government applications of ML can draw on multiple sources of data, potentially including users' and clients' sensitive data. We provide a comprehensive survey of contemporary advances on several fronts, covering involuntary data leakage which is natural to ML models, potential malevolent leakage which is caused by privacy attacks, and currently available defence mechanisms. We focus on inference-time leakage, as the most likely scenario for publicly available models. We first discuss what leakage is in the context of different data, tasks, and model architectures. We then propose a taxonomy across involuntary and malevolent leakage, available defences, followed by the currently available assessment metrics and applications. We conclude with outstanding challenges and open questions, outlining some promising directions for future research.

FatNet: A Feature-attentive Network for 3D Point Cloud Processing

The application of deep learning to 3D point clouds is challenging due to its lack of order. Inspired by the point embeddings of PointNet and the edge embeddings of DGCNNs, we propose three improvements to the task of point cloud analysis. First, we introduce a novel feature-attentive neural network layer, a FAT layer, that combines both global point-based features and local edge-based features in order to generate better embeddings. Second, we find that applying the same attention mechanism across two different forms of feature map aggregation, max pooling and average pooling, gives better performance than either alone. Third, we observe that residual feature reuse in this setting propagates information more effectively between the layers, and makes the network easier to train. Our architecture achieves state-of-the-art results on the task of point cloud classification, as demonstrated on the ModelNet40 dataset, and an extremely competitive performance on the ShapeNet part segmentation challenge.

Divided We Stand: A Novel Residual Group Attention Mechanism for Medical Image Segmentation

Given that convolutional neural networks extract features via learning convolution kernels, it makes sense to design better kernels which can in turn lead to better feature extraction. In this paper, we propose a new residual block for convolutional neural networks in the context of medical image segmentation. We combine attention mechanisms with group convolutions to create our group attention mechanism, which forms the fundamental building block of FocusNetAlpha - our convolutional autoencoder. We adapt a hybrid loss based on balanced cross entropy, tversky loss and the adaptive logarithmic loss to create a loss function that converges faster and more accurately to the minimum solution. On comparison with the different residual block variants, we observed a 5.6% increase in the IoU on the ISIC 2017 dataset over the basic residual block and a 1.3% increase over the resneXt group convolution block. Our results show that FocusNetAlpha achieves state-of-the-art results across all metrics for the ISIC 2018 melanoma segmentation, cell nuclei segmentation and the DRIVE retinal blood vessel segmentation datasets with fewer parameters and FLOPs. Our code and pre-trained models will be publicly available on GitHub to maximize reproducibility.